Hi, I am a bit unsure whether I have correctly understood the help page of normaliseIllumina (of package beadarray) with regards to the question when this function logarithmizes the expression data. The help page says: Note: If your 'BSData' object contains data already on the log-scale, be careful that you choose an appropriate 'transform' to avoid logging it twice. The same applies for the '"vst"' transformation and '"vsn"' normalisation methods which require the expression data stored in 'BSData' to be on the original (un-logged) scale. Does with mean that a transformation to log scale (via log or glog) happens _only_ when 'transform' is 'log2' or 'vst' or 'method' is 'vsn'? Does it mean furthermore that for 'method="vsn"', 'transform' _must_ be set to 'none' to avoid double logarithmizing? Thanks Simon +--- | Dr. Simon Anders, Dipl.-Phys. | European Bioinformatics Institute, Hinxton/Cambridge, UK | office phone +44-1223-494478, mobile phone +44-7942-583830 | preferred (permanent) e-mail: sanders at fs.tum.de

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